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### Running command:
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###   /home/rapidbuild/bbs-3.24-bioc-rapid/R/bin/Rscript -e "BiocCheck::BiocCheck('ChemmineR_3.65.0.tar.gz','quit-with-status'=TRUE)"
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── Installing ChemmineR ────────────────────────────────────────────────────────
✔ Package installed successfully
── ChemmineR session metadata ──────────────────────────────────────────────────
→ sourceDir: /tmp/RtmpTJdOMB/file2c20285feb9ef6/ChemmineR
→ BiocVersion: 3.24
→ Package: ChemmineR
→ PackageVersion: 3.65.0
→ BiocCheckDir: /media/volume/teran2_disk/rapidbuild/bbs-3.24-bioc-rapid/meat/ChemmineR.BiocCheck
→ BiocCheckVersion: 1.49.4
→ sourceDir: /tmp/RtmpTJdOMB/file2c20285feb9ef6/ChemmineR
→ installDir: /tmp/RtmpTJdOMB/file2c20286d2b2490
→ isTarBall: TRUE
→ platform: unix
── Running BiocCheck on ChemmineR ──────────────────────────────────────────────
* Checking for deprecated package usage...
* Checking for remote package usage...
* Checking for 'LazyData: true' usage...
* Checking version number...
* Checking for version number mismatch...
* Checking version number validity...
* Checking R version dependency...
ℹ NOTE: Update R version dependency from 2.10.0 to 4.6.0
* Checking package size...
* Checking individual file sizes...
* Checking biocViews...
* Checking that biocViews are present...
* Checking package type based on biocViews...
→ Software
* Checking for non-trivial biocViews...
* Checking that biocViews come from the same category...
* Checking biocViews validity...
* Checking for recommended biocViews...
ℹ NOTE: Consider adding these automatically suggested biocViews: Classification
ℹ Search 'biocViews' at https://contributions.bioconductor.org
* Checking build system compatibility...
* Checking for proper Description: field...
* Checking if DESCRIPTION is well formatted...
* Checking for whitespace in DESCRIPTION field names...
* Checking if 'Package:' field matches directory / tarball...
* Checking for Version: field...
✖ ERROR: Remove Maintainer field. Use Authors@R [cre] designation.
* Checking License: for restrictive use...
* Checking for recommended DESCRIPTION fields...
ℹ NOTE: Provide 'BugReports' field(s) in DESCRIPTION
* Checking for Bioconductor software dependencies...
ℹ Bioconductor dependencies found in Imports & Depends (6%).
* Checking for pinned package versions in DESCRIPTION...
* Checking for 'fnd' role in Authors@R...
ℹ NOTE: No 'fnd' role found in Authors@R. If the work is supported by a grant,
consider adding the 'fnd' role to the list of authors.
* Checking NAMESPACE...
✖ ERROR: 'NAMESPACE' contains exportPattern with '[[:alpha:]]'; use explicit
exports instead.
* Checking .Rbuildignore...
* Checking for stray BiocCheck output folders...
* Checking vignette directory...
✖ ERROR: 'VignetteBuilder' listed in DESCRIPTION but not found as
'VignetteEngine' in any vignettes:
  • knitr
! WARNING: Vignette(s) missing Vignette metadata. See
https://r-pkgs.org/vignettes.html
  Update the following files:
    • ChemmineR.Rmd
✖ ERROR: 'VignetteEngine' specified but not in the DESCRIPTION.
  Add 'VignetteEngine' to DESCRIPTION from the following:
    • vignettes/ChemmineR.Rmd
! WARNING: Package listed as VignetteEngine or VignetteBuilder but not
currently Suggested.
  Add the following to Suggests in DESCRIPTION:
    • %knitr
! WARNING: Vignette(s) missing '\%VignetteIndexEntry{Vignette Title}'.
  Update the following files:
    • ChemmineR.Rmd
! WARNING: Evaluate more vignette chunks.
ℹ 97 out of 183 code chunks = 53% unevaluated
ℹ 
ℹ NOTE: Vignette(s) found with missing chunk labels
  Found in files:
    • ChemmineR.Rmd
! WARNING: Avoid T/F variables; If logical, use TRUE/FALSE
  Found in files:
    • vignettes/ChemmineR.Rmd (chunk no. 107, line 1491, column 48)
    • vignettes/ChemmineR.Rmd (chunk no. 165, line 2280, column 60)
* Checking package installation calls in R code...
* Checking for library/require of ChemmineR...
! WARNING: Avoid the use of 'library' or 'require' in R code
  Found in files:
    • require() in R/compound_db.R (line 18, column 17)
    • ...
    • require() in R/sim.R (line 574, column 29)
* Checking coding practice...
ℹ NOTE: Avoid sapply(); use vapply()
  Found in files:
    • R/AllClasses.R (line 191, column 41)
    • ...
    • R/sim.R (line 1054, column 24)
ℹ NOTE: Avoid 1:...; use seq_len() or seq_along()
  Found in files:
    • AllClasses.R (line 43, column 30)
    • ...
    • sim.R (line 1033, column 45)
ℹ NOTE: Avoid 'cat' and 'print' outside of 'show' methods
  Found in files:
    • cat() in R/AllClasses.R (line 114, column 9)
    • ...
    • cat() in R/sim.R (line 437, column 9)
ℹ NOTE: Avoid using '=' for assignment and use '<-' instead
  Found in files:
    • R/AllClasses.R (line 32, column 25)
    • ...
    • R/sim.R (line 1062, column 23)
ℹ NOTE: Avoid the use of 'paste' in condition signals
  Found in files:
    • R/AllClasses.R (line 695, column 36)
    • ...
    • R/postgresql.R (line 37, column 21)
ℹ NOTE: Avoid redundant 'stop' and 'warn*' in signal conditions
  Found in files:
    • R/compound_db.R (line 65, column 28)
    • ...
    • R/compound_db.R (line 880, column 64)
! WARNING: Avoid T/F variables; If logical, use TRUE/FALSE
  Found 9 times:
    • T in R/AllClasses.R (line 2030, column 139)
    • ...
    • F in R/sim.R (line 542, column 52)
! WARNING: Avoid class membership checks with class() / is() and == / !=; Use
is(x, 'class') for S4 classes
  Found in files:
    • AllClasses.R (line 42, column 30)
    • ...
    • pubchem_calls.R (line 176, column 25)
ℹ NOTE: Avoid system() ; use system2()
  Found in files:
    • system() in R/AllClasses.R (line 14, column 9)
    • system() in R/AllClasses.R (line 15, column 9)
* Checking parsed R code in R directory, examples, vignettes...
ℹ NOTE: Avoid '<<-' if possible (found 21 times)
  • <<- in R/AllClasses.R (line 1505, column 78)
  • ...
  • <<- in R/sim.R (line 432, column 27)
ℹ NOTE: Avoid 'suppressWarnings'/'*Messages' if possible (found 10 times)
  • suppressWarnings() in R/AllClasses.R (line 2492, column 33)
  • ...
  • suppressWarnings() in R/sim.R (line 574, column 12)
* Checking function lengths...
ℹ NOTE: The recommended function length is 50 lines or less. There are 24
functions greater than 50 lines.
  The longest 5 functions are:
    • .parseV3000() (R/AllClasses.R): 180 lines
    • ...
    • cluster.visualize() (R/cluster.R): 111 lines
* Checking man page documentation...
ℹ NOTE: Auto-generated '%% ~' comments found in Rd man pages.
  • man/nearestNeighbors.Rd
  • man/SDFstr-class.Rd
! WARNING: Empty or missing \value sections found in man page(s).
  Found in files:
    • man/openBabelPlot.Rd
    • ...
    • man/write.SMI.Rd
✖ ERROR: At least 80% of man pages documenting exported objects must have
runnable examples.
  The following pages do not:
    • addDescriptorType.Rd
    • ...
    • toolDetails.Rd
ℹ NOTE: Usage of dontrun / donttest tags found in man page examples. 33% of man
pages use at least one of these tags.
  Found in files:
    • addDescriptorType.Rd
    • ...
    • write.SDFsplit.Rd
ℹ NOTE: Use donttest instead of dontrun.
  Found in files:
    • addDescriptorType.Rd
    • ...
    • write.SDFsplit.Rd
* Checking package NEWS...
* Checking unit tests...
* Checking skip_on_bioc() in tests...
* Checking formatting of DESCRIPTION, NAMESPACE, man pages, R source, and
vignette source...
ℹ NOTE: Consider shorter lines; 1254 lines (7%) are > 80 characters long.
  First few lines:
    • R/AllClasses.R#L13 .sdfDownload <- function(mypath="ftp://f ...
    • ...
    • vignettes/ChemmineR.Rmd#L2564 Foundation: [ABI-0957099](http://www.nsf
    ...
ℹ NOTE: Consider 4 spaces instead of tabs; 4383 lines (26%) contain tabs.
  First few lines:
    • R/AllClasses.R#L6 # http://www.symyx.com/downloads/public ...
    • ...
    • vignettes/ChemmineR.Rmd#L2297 density.info="none", trace="none") ...
ℹ NOTE: Consider multiples of 4 spaces for line indents; 1142 lines (7%) are
not.
  First few lines:
    • R/AllClasses.R#L164 if(nchar(gsub("\\d| ", "", substring( ...
    • ...
    • vignettes/ChemmineR.Rmd#L2555 sessionInfo() ...
ℹ See https://contributions.bioconductor.org/r-code.html
ℹ See styler package: https://cran.r-project.org/package=styler as described in
the BiocCheck vignette.
* Checking if package already exists in CRAN...
* Checking for bioc-devel mailing list subscription...
ℹ NOTE: Cannot determine whether maintainer is subscribed to the Bioc-Devel
mailing list (requires admin credentials). Subscribe here:
https://stat.ethz.ch/mailman/listinfo/bioc-devel
* Checking for support site registration...
ℹ Maintainer is registered at support site.
✖ ERROR: Add package to Watched Tags in your Support Site profile; visit
https://support.bioconductor.org/accounts/edit/profile
── BiocCheck v1.49.4 results ───────────────────────────────────────────────────
✖ 6 ERRORS | ⚠ 9 WARNINGS | ℹ 22 NOTES
ℹ See the ChemmineR.BiocCheck folder and run
  browseVignettes(package = 'BiocCheck')
  for details.